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  4. Transcriptomic analysis of skeletal muscle regeneration across mouse lifespan

Transcriptomic analysis of skeletal muscle regeneration across mouse lifespan

File(s)
Walter_cornellgrad_0058F_14391.pdf (12.47 MB)
ExtendedDataFile1.csv (5.09 KB)
ExtendedDataFile2.xlsx (1.88 MB)
Permanent Link(s)
https://doi.org/10.7298/wp8t-p283
https://hdl.handle.net/1813/116607
Collections
Cornell Theses and Dissertations
Author
Walter, Lauren
Abstract

Skeletal muscle regeneration relies on the orchestrated interaction of myogenic and non-myogenic cells with spatial and temporal coordination. The regenerative capacity of skeletal muscle declines with aging due to alterations in myogenic stem/progenitor cell states and functions, non-myogenic cell contributions, and systemic changes, all of which accrue with age. A holistic network-level view of the cell-intrinsic and -extrinsic changes influencing muscle stem/progenitor cell contributions to muscle regeneration across lifespan remains poorly resolved. To provide a comprehensive atlas of regenerative muscle cell states across mouse lifespan, we collected a compendium of >270,000 single-cell transcriptomes from hindlimb muscles of young, old, and geriatric (4-26 months-old) mice at six closely sampled time-points following myotoxin injury. We identified 29 muscle-resident cell types, eight of which exhibited accelerated or delayed dynamics in their abundances between age groups, including T and NK cells and multiple monocyte/macrophage subtypes, suggesting that the age-related decline in muscle repair may arise from temporal miscoordination of the inflammatory response. We performed a pseudotime analysis of myogenic cells across the regeneration timespan and found age-specific myogenic stem/progenitor cell trajectories in old and geriatric muscles. Given the critical role that cellular senescence plays in limiting cell contributions in aged tissues, we built a series of tools to bioinformatically identify senescence in these single-cell data and assess their ability to identify senescence within key myogenic stages. By comparing single-cell senescence scores to co-expression of hallmark senescence genes Cdkn2a and Cdkn1a, we found that a gene list experimentally derived from a muscle foreign body response (FBR) fibrosis model accurately identified senescent-like myogenic cells across mouse ages, injury time-points, and cell-cycle states, in a manner comparable to curated gene lists. Further, this scoring approach in both single-cell and spatial transcriptomic datasets pinpointed transitory senescent-like subsets within the myogenic stem/progenitor cell trajectory that are associated with stalled MuSC self-renewal states across all ages of mice. This new resource of mouse skeletal muscle aging provides a comprehensive portrait of the changing cellular states and interactions underlying skeletal muscle regeneration across mouse lifespan.

Description
159 pages
Supplemental file(s) description: Summary of Senescence Signature gene lists, Summary of scRNA-seq samples.
Date Issued
2024-08
Keywords
aging
•
myogenesis
•
scRNA
•
senescence
•
skeletal muscle
•
spatial transcriptomics
Committee Chair
Cosgrove, Benjamin
Committee Member
De Vlaminck, Iwijn
Lee, Siu
Degree Discipline
Genetics, Genomics and Development
Degree Name
Ph. D., Genetics, Genomics and Development
Degree Level
Doctor of Philosophy
Rights
Attribution-NonCommercial-NoDerivatives 4.0 International
Rights URI
https://creativecommons.org/licenses/by-nc-nd/4.0/
Type
dissertation or thesis
Link(s) to Catalog Record
https://newcatalog.library.cornell.edu/catalog/16611802

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